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PHITS Voxel Phantom: Multi-Purpose Code System

Reproduce complex structures like the human body using repeated rectangles filled with materials in PHITS. Learn how to make voxel phantoms in virtual space and conduct calculations for therapies. Understand Universe and Lattice functions for high-resolution results.

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PHITS Voxel Phantom: Multi-Purpose Code System

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  1. PHITS Multi-Purpose Particle and Heavy Ion Transport code System Making Voxel Phantom Aug. 2014 revised title 1

  2. What is Voxel Phantom? Reproduce a complex structure such as human body based on repeated rectangles filled with a certain material (See Manual 5.7.5) You can make voxel phantom in PHITS virtual space using Universeand Latticefunctions (See Manual 5.7.3 and 5.7.4) Low resolution High resolution Introduction 2

  3. Examples of PHITS calculations using voxel phantom Biological dose estimation for charged-particle therapy T. Sato et al. Radiat. Res. (2009) Treatment planning for BNCT H. Kumada et al. J. Phys.: Conf. Ser. (2007) Introduction 3

  4. Table of Contents • Universe • Lattice • Simple voxel phantom • Conversion from DICOM format • Summary • Appendix Table of Contents 4

  5. What is Universe? → Virtual space in PHITS You can define many universes in PHITS virtual space Universe1 But only 1 universe (main space) is the stage of particle transport simulation Other universes are used for replacing some parts of the main space using “fill” command Main space Some parts of the main space (inside the boxes) are filled with universe 1 Universe 5

  6. Example of Universe always void universe.inp [ C e l l ] $ Main space 1 0 11 -12 13 -14 15 -17 FILL=1 2 0 11 -12 13 -14 17 -16 FILL=2 9 -1 #1 #2 $ Universe 1 101 1 -1.00 -10 13 -14 U=1 102 0 #101 U=1 $ Universe 2 201 2 -7.86 -10 13 -14 U=2 202 1 -1.00 #201 U=2 [ S u r f a c e ] 10 CY 5 11 PX -6 12 PX 6 13 PY -6 14 PY 6 15 PZ -6 16 PZ 6 17 PZ 0 Filled with Universe1 Declare universe 1 PX -3 PX 9 Figure 5.13 (a) Two rectangular solids. (b) Cylinder filled with water. (c) Iron cylinder in water Universe 6

  7. Table of Contents • Universe • Lattice • Simple voxel phantom • Conversion from DICOM format • Summary • Appendix Table of Contents 7

  8. What is Lattice? → Repeated structure used in PHITS virtual space It is troublesome to define all surfaces and cells used in repeated structure Define only surfaces and cells used in fundamental structure Examples of Lattice in PHITS Express the repeated structure using “lat” command Lattice 8

  9. How to define lattice? You cannot directly define the contents inside lattice Only repeated structure can be defined in lattice universe It is better to define lattice not in main space but in a universe You have to fill lattice with other universe Define repeated structure using more than 2 universes fill fill Universe1 (Lattice structure) Universe2 (fundamental structure) Main space Lattice 9

  10. PHITS input lattice.inp [ S u r f a c e ] 1 rpp -5 5 -5 5 -1 1 2 rpp -6 6 -6 6 -2 1 99 so 100 101 rpp -1 1 -1 1 -1 1 201 sph 0 0 0 1 [ C e l l ] $ Main space 1 3 -8.96 1 -2 2 0 -1 fill=1 98 0 -99 2 99 -1 99 $ Universe 1 101 0 -101 lat=1 u=1 fill=-2:2 -2:2 0:0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 $ Universe 2 201 1 -19.32 -201 u=2 202 0 201 u=2 （2,2,0） -5Y5 Basic lattice（0,0,0） （-2,-2,0） -5X5 Region 101 Declare lattice type 1 (Rectangle) Define the region of basic lattice Define the number of repeated structure Universe number to be filled with（5×5×1 matrix） Location should be adjusted to that of the basic lattice Lattice 10

  11. Change the contents of lattice lattice1.inp Change 1st box from golden ball to void [ C e l l ] $ Main space 1 3 -8.96 1 -2 2 0 -1 fill=1 98 0 -99 2 99 -1 99 $ Universe 1 101 0 -101 lat=1 u=1 fill=-2:2 -2:2 0:0 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 $ Universe 2 201 1 -19.32 -201 u=2 202 0 201 u=2 $ Universe 3 302 0 -99 u=3 After (lattice1.inp) Before (lattice.inp) Lattice 11

  12. Table of Contents • Universe • Lattice • Simple voxel phantom • Conversion from DICOM format • Summary • Appendix Table of Contents 12

  13. How to define voxel phantom? ①　Make universes filled with an unique material such as bone and soft tissue Universe1 (void) Universe2 (water) Universe3 (Aluminum) ②　Make voxel phantom by repeating those universes ③　Fill some part of the main space with the voxel phantom Universe10 (Voxel Phantom) Main Space Simple Voxel Phantom 13

  14. PHITS input file robot.inp Surfaces for the basic lattice [ S u r f a c e ] $ fundamental voxel 1 px -5 2 px -3 3 py 3 4 py 5 5 pz 3 6 pz 5 99 so 100 $ Main space 201 rpp -5 5 -5 5 -5 5 202 rcc 0 0 -5 0 0 4 8 203 rcc 0 0 -6 0 0 5 9 [ C e l l ] $ Material universe 1 0 -99 u=1 2 1 -1.00 -99 u=2 3 2 -2.70 -99 u=3 $ Voxel universe 101 0 -101 lat=1 u=10 fill=0:4 0:4 0:4 1 1 1 1 1 1 2 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 … repeat 4 times $ Main space 201 0 -201 fill=10 202 0 201 -202 203 3 -8.96 202 -203 204 0 -99 201 203 205 -1 99 Any large region is OK Lattice order: X+, Y+, Z+ (start with left&lower voxel) z y x Simple Voxel Phantom 14

  15. Change materials robot1.inp [ C e l l ] $ Material universe 1 0 -99 u=1 2 1 -1.00 -99 u=2 3 2 -2.70 -99 u=3 4 3 -8.96 -99 u=4 $ Voxel universe 101 0 -2 1 3 -4 5 -6 lat=1 u=10 fill=0:4 0:4 0:4 ... last one 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 1 1 1 1 … repeat 4 times $ Main space 201 0 -201 fill=10 202 0 201 -202 203 3 -8.96 202 -203 204 0 -99 201 203 205 -1 99 Change the material of the phantom head from water to copper Before (robot.inp) After (robot1.inp) Simple Voxel Phantom 15

  16. Example of dose calculation robot-heat-xz.eps robot-heat-reg.out x: Serial Num. of Region y: Heat [MeV/source] h: x n n y(total),l3 n # num reg volume heat r.err 1 2 1.0000E+00 9.5978E-01 0.1277 2 3 1.0000E+00 3.4847E+01 0.0000 3 4 1.0000E+00 5.1924E+01 0.0000 [t-heat] tallyusing mesh = reg Calculate dose for each region (Head, torso, and arm&leg) [t-heat] tally using mesh = xyz Useful for calculating dose inside tumor region Visualize the dose distribution Simple Voxel Phantom 16

  17. Table of Contents • Universe • Lattice • Simple voxel phantom • Conversion from DICOM format • Summary • Appendix Table of Contents 17

  18. DICOMformat (Binary) Data for 1 slice （sample001.dcm） ①　Header (Information on time, voxel size etc.) ②　CT values（1,1→2,1→3,1→…→nx-1, ny → nx, ny） Several files are contained in one folder to represent an object 3D view cross sectional view It is necessary to convert from DICOM to PHITS-input format (CT value, binary) (Universe number, text) Dicom to PHITS 18

  19. Conversion (DICOM2PHITS) Convert from Dicom data to PHITS input format (voxel phantom) Refer to “PHITS Tutorial How to use DICOM2PHITS” phits/utility/dicom2phits/phits-lec-dicom2phits-jp.ppt 1. Make an input file for DICOM2PHITS （dicom2phits.inp） "data/HumanVoxelTable.data" Conversion table "DICOM/" DICOM files are automatically identified in this directory "PHITSinputs" Directory for PHITS inputs to be created 1 20 Slices to be used (1<=z<=20) 70 430 90 460 Clipping (70<=x<=430, 90<=y<=460) 4 4 1 Coarse graining (Average on 4 times 4 voxels in x and y direction) 0 Origin option: 0:Center of data 1:Reading from DICOM header 0 PHITS parameter: 0:Minimal 1:Photon therapy 2:Particle therapy 1 Reading slice order: +1:Ascending order or -1:Descending order 2.Execute Windows: Drag dicom2phits.inpand drop into dicom2phits.bat Mac:Double click dicom2phits.command and type dicom2phits.inp+ enter A sample input file will be created in PHITSinputs/ directory DICOM2PHITS HowTo 19

  20. Reduce computational time Purpose Every time PHITS runs… It converts its input file to binary, and re-reads the binary file It is better to… Make binary file of voxel phantom prior to the PHITS execution Procedure ①　Insert the following 2 lines in the [Parameters] section ivoxel = 2 # Convert the “fill” part of lattice to binary and output to file(18) file(18) = voxel.bin # Output file name for binary voxel phantom ②　Execute PHITS →Binary file was successfully generated!! ③　Change “ivoxel = 1”, and comment out “infl” command ivoxel = 1# Read the “fill” part of lattice from file(18) Speed up! $ infl:{voxel1.inp} Dicom to PHITS 20

  21. Table of Contents • Universe • Lattice • Simple voxel phantom • Conversion from DICOM format • Summary • Appendix Table of Contents 21

  22. Summary • Voxel phantom can be implemented in PHITS using Universe and Lattice concepts • DICOM format must be converted into PHITS input format using DICOM2PHITS • Computational time can be reduced by using “ivoxel” parameter Summary 22

  23. Table of Contents • Universe • Lattice • Simple voxel phantom • Conversion from DICOM format • Summary • Appendix Table of Contents 23

  24. How to Deal with High-Resolution Phantom? High resolution voxel phantom requires numerous memory Default setting of PHITS is allowed to use memory only less than 2 Byte e.g.) Whole body voxel phantom (180cm×30cm×50cm) with 1mm3 resolution consists of 270,000,000 voxels, and costs 5.4GByte memory, since PHITS uses memory approximately 20 Byte / voxel How to deal with the situation? Change “param.inc” included in “src” folder • increase mdas: Maximum memory allowed to be used by PHITS (Byte) / 8 • increase latmax:Maximum number of lattice in a cell • declare integer*8 for several parameters (see next page in detail) Delete all object files (*.o) and re-compile PHITS* Memory is insufficient? Divide voxel phantom into several regions to reduce the area to be voxelized Combine several CT pixels into one voxel to decrease the resolution of phantom *For Windows PC, gfortran is recommended to be used for this purpose, because PHITS executable file compiled by Intel Fortran may cause “stack overflow” for large voxel phantom 24

  25. How to Deal with High-Resolution Phantom? If #voxels is greater than 50 millions, many changes are necessary e.g. total #voxel = 150 millions, max #voxel per cell = 40 millions Change include files in “src” folder param.inc integer*8 mdas,mcmx,mci,mmdas,mmmax,nbnds,mct ! avoid overflow (integer*4 =< 2147483647） parameter ( mdas = 500000000 )! Maximum memory allowed to be used by PHITS (Byte) / 8 parameter ( latmax = 47000000 ) ! Maximum number of lattice in a cell angel00.inc integer*8 mdas,mmdas,mmmax ! avoid overflow (integer*4 =< 2147483647） parameter ( mdas = 350000000 )! Maximum memory allowed to be used by ANGEL (Byte) / 8 Add compiler options （e.g. for Intel Fortran in Linux） makefile F77 = ifort FCFLAGS = -noautomatic -mcmodel=large -i-dynamic -i-dynamic: Dynamic link to libraries -mcmodel=large: no limitation in memory use (this option is only valid for Linux) Appendix 25

  26. Change the order of lattice lattice2.inp [ S u r f a c e ](pick up partially) 101 px -1 102 px 1 103 py -1 104 py 1 105 pz -1 106 pz 1 [ C e l l ](pick up partially) $ Universe 1 101 0 -102 101 -104 103 -106 105 lat=1 u=1 fill=-2:2 -2:2 0:0 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 Same as RPP, BOX RPP is divided into each surface -102101 -104 103 -106 105 X:+, Y:+, Z:+ 101-102 -104 103 -106 105 X: –, Y:+, Z: + Order is important! Prior surface faces to the forward direction -102101 103 -104 -106 105 X: +, Y: –, Z:+ 101-102 103 -104 -106 105 X: –, Y: –, Z: + Appendix 26

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